Admittedly, I was being a bit tongue in cheek about it.
The thing I see in DS9 is not only a science vs. faith one, it's also rationality vs. irrationality. Bajorans are often portrayed as irrational beings, blinded
by their faith, while the Starfleet officers keep their calm and keep an open mind. They question the Prophets, while the Bajorans blindly follow them, for example. Sadly, I see that in real life as well. It's a big part of religion and faith to just blindly throw yourself into something.
So in DS9 it doesn't really truly matter that they can scientifically measure the existence of the Prophets, it's simply that their mindset is different and they're mostly incapable of blind faith. Major Kira represents an enlightened believer who doesn't take everything for granted, while Kai Winn represents a hardcore fundamentalist who blindly follows everything without questioning it. Sisko is somewhere in between. We can clearly see that everytime he gives in to the Prophets, he entirely stops being rational.